Single-cell spatial transcriptomic profiling defines a pathogenic inflammatory niche in chronic active multiple sclerosis lesions - snRNA-seq

Compartmentalized inflammation is considered a critical factor in driving the progression of multiple sclerosis (MS). Yet, the mechanisms sustaining its persistence remain poorly understood. A hallmark of this persistent and slowly evolving inflammatory process are chronic active MS lesions. In this study, we created a high-resolution, single-cell molecular and spatial atlas of chronic inflammation in MS. To accomplish this, we combined single-nucleus RNA sequencing (snRNA-seq) with single-cell spatial transcriptomics using multiplexed error-robust fluorescence in situ hybridization (MERFISH) to examine MS lesions, specifically focusing on those exhibiting chronic active immune pathology characterized by lymphocyte presence. Our integrative profiling uncovered the molecular landscape of glial and immune cells, their disease-associated states, and the surrounding microenvironments. Within the lesion rim, we identified CD8+ T cell niches with inflamed, foamy microglia, characterized by an interferon response and dysfunctional lipid metabolism. To investigate the function of these microglia, we deleted ATP-binding cassette transporters A1 and G1 (ABCA1/G1) in microglia of mice and induced experimental autoimmune encephalomyelitis (EAE). Our findings revealed that inhibiting cholesterol efflux increased the formation of lipid-storing phagocytes, which actively drove inflammatory processes in EAE. Moreover, we found that pharmacologically targeting sterol metabolism presents a promising therapeutic strategy for mitigating inflammation in EAE. Thus, we have created a high-resolution map of immune niches in chronic active MS lesions, leading to the discovery of lipid-associated microglia as key drivers of neuroinflammation.